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  Quantifying the tissue-specific regulatory information within enhancer DNA sequences

Benner, P., & Vingron, M. (2021). Quantifying the tissue-specific regulatory information within enhancer DNA sequences. NAR: genomics and bioinformatics, 3(4): lqab095. doi:10.1093/nargab/lqab095.

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 Creators:
Benner, Philipp1, Author              
Vingron, Martin1, Author              
Affiliations:
1Transcriptional Regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Recent efforts to measure epigenetic marks across a wide variety of different cell types and tissues provide insights into the cell type-specific regulatory landscape. We use these data to study whether there exists a correlate of epigenetic signals in the DNA sequence of enhancers and explore with computational methods to what degree such sequence patterns can be used to predict cell type-specific regulatory activity. By constructing classifiers that predict in which tissues enhancers are active, we are able to identify sequence features that might be recognized by the cell in order to regulate gene expression. While classification performances vary greatly between tissues, we show examples where our classifiers correctly predict tissue-specific regulation from sequence alone. We also show that many of the informative patterns indeed harbor transcription factor footprints.

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Language(s): eng - English
 Dates: 2021-09-282021-10-27
 Publication Status: Published online
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 Rev. Type: -
 Identifiers: DOI: 10.1093/nargab/lqab095
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Title: NAR: genomics and bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 3 (4) Sequence Number: lqab095 Start / End Page: - Identifier: ISSN: 2631-9268
CoNE: https://pure.mpg.de/cone/journals/resource/2631-9268